FSL-MRS Voxel Location

Hi all!

We recently implemented a processing pipeline for processing .7 MRS files from a 3T GE scanner, specifically looking at SVS in the left-frontal region. However, for some reason, the ‘voxel location’ image displays the voxel as being on the right side / contralateral side of acquisition (this was confirmed by checking the original voxel placement done at the scanning center, which showed up on the left frontal region).

Curious if anyone else has run into the problem or has any suggestions on how to potentially resolve this - Thanks!

Hi @jharoon,

How do things look in fsleyes? If this is still wrong, it might be related to an issue I’m part way through fixing. See Conversion failure on GE data · Issue #123 · wtclarke/spec2nii · GitHub

Hi William,

Thanks for the quick response! I’m attaching a png of the voxel placement, post-processing in FSL_mrs. The voxel at acquisition was placed on the left side, but for all of our cases that we’ve processed, the FSL voxel placement seems to flip the orientation.

Yes, I understand, but, as asked above, please load the data into fsleyes and see where the voxel is positioned. The fsleyes code is much more heavily validated, and therefore will indicate whether it is an issue with data conversion or the plotting code in FSL-MRS.

Ah understood, apologies! It looks like when the voxel nifti data is loaded into FSLeyes with the T1, it does appear on the correct side, but it is only after processing that it appears on the opposite side.

Thanks for checking. Could you run fslreorient2std on the T1 before passing it to the processing and then see whether that makes a difference for the case when it gets the wrong side?

Thanks for the suggestion! Unfortunately, tried it on two cases and that didn’t seem to work either